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Bacon" Date: Thu, 14 Mar 2019 23:59:48 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r495746 - in head/biology/cd-hit: . files X-SVN-Group: ports-head X-SVN-Commit-Author: jwb X-SVN-Commit-Paths: in head/biology/cd-hit: . files X-SVN-Commit-Revision: 495746 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Rspamd-Queue-Id: 0A39174A45 X-Spamd-Bar: -- Authentication-Results: mx1.freebsd.org X-Spamd-Result: default: False [-2.96 / 15.00]; local_wl_from(0.00)[FreeBSD.org]; NEURAL_HAM_MEDIUM(-1.00)[-0.998,0]; NEURAL_HAM_LONG(-1.00)[-1.000,0]; NEURAL_HAM_SHORT(-0.97)[-0.967,0]; ASN(0.00)[asn:11403, ipnet:2610:1c1:1::/48, country:US] X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Thu, 14 Mar 2019 23:59:49 -0000 Author: jwb Date: Thu Mar 14 23:59:47 2019 New Revision: 495746 URL: https://svnweb.freebsd.org/changeset/ports/495746 Log: biology/cd-hit: Upgrade to 4.8.1 Convert Makefile REINPLACE to patch for sending upstream Added: head/biology/cd-hit/files/ head/biology/cd-hit/files/patch-Makefile (contents, props changed) Modified: head/biology/cd-hit/Makefile head/biology/cd-hit/distinfo head/biology/cd-hit/pkg-plist Modified: head/biology/cd-hit/Makefile ============================================================================== --- head/biology/cd-hit/Makefile Thu Mar 14 23:53:47 2019 (r495745) +++ head/biology/cd-hit/Makefile Thu Mar 14 23:59:47 2019 (r495746) @@ -1,33 +1,29 @@ # $FreeBSD$ -PORTNAME= cd-hit -PORTVERSION= 4.6.6 -PORTREVISION= 5 +PORTNAME= cd-hit DISTVERSIONPREFIX= V -CATEGORIES= biology +DISTVERSION= 4.8.1 +CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Clustering and comparing protein or nucleotide sequences LICENSE= GPLv2 +USES= compiler:openmp gmake shebangfix USE_GITHUB= yes + GH_ACCOUNT= weizhongli GH_PROJECT= cdhit - -USES= compiler:openmp gmake shebangfix SHEBANG_FILES= ${WRKSRC}/*.pl MAKE_FLAGS= openmp=yes post-patch: @${REINPLACE_CMD} \ - -e 's|g++|${CXX}|g' \ - -e 's|\$$(PREFIX)|$${DESTDIR}$${PREFIX}/bin|g' \ - ${WRKSRC}/${MAKEFILE} - @${REINPLACE_CMD} \ -e 's|/bin/bash|${LOCALBASE}/bin/bash|g' \ - ${WRKSRC}/*.pl + ${WRKSRC}/cd-hit-2d-para.pl \ + ${WRKSRC}/cd-hit-para.pl post-install: @cd ${STAGEDIR}${PREFIX}/bin && \ Modified: head/biology/cd-hit/distinfo ============================================================================== --- head/biology/cd-hit/distinfo Thu Mar 14 23:53:47 2019 (r495745) +++ head/biology/cd-hit/distinfo Thu Mar 14 23:59:47 2019 (r495746) @@ -1,3 +1,3 @@ -TIMESTAMP = 1482076217 -SHA256 (weizhongli-cdhit-V4.6.6_GH0.tar.gz) = a0c89c969ad338f958620083b12bc69fa30fcba8246a7ec0b6243e5b2ba0365d -SIZE (weizhongli-cdhit-V4.6.6_GH0.tar.gz) = 1149112 +TIMESTAMP = 1552053543 +SHA256 (weizhongli-cdhit-V4.8.1_GH0.tar.gz) = f8bc3cdd7aebb432fcd35eed0093e7a6413f1e36bbd2a837ebc06e57cdb20b70 +SIZE (weizhongli-cdhit-V4.8.1_GH0.tar.gz) = 945639 Added: head/biology/cd-hit/files/patch-Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/cd-hit/files/patch-Makefile Thu Mar 14 23:59:47 2019 (r495746) @@ -0,0 +1,92 @@ +--- Makefile.orig 2019-02-28 20:13:59 UTC ++++ Makefile +@@ -1,6 +1,6 @@ +-CC = g++ -Wall -ggdb +-CC = g++ -pg +-CC = g++ ++CXX ?= g++ -Wall -ggdb ++CXX ?= g++ -pg ++CXX ?= g++ + + # default with OpenMP + # with OpenMP +@@ -47,7 +47,7 @@ PROGS = cd-hit cd-hit-est cd-hit-2d cd-h + CCFLAGS := $(CPPFLAGS) $(CCFLAGS) $(CXXFLAGS) + + .c++.o: +- $(CC) $(CCFLAGS) -c $< ++ $(CXX) $(CCFLAGS) -c $< + + all: $(PROGS) + +@@ -57,52 +57,53 @@ clean: + # programs + + cd-hit: cdhit-common.o cdhit-utility.o cdhit.o +- $(CC) $(CCFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit ++ $(CXX) $(CCFLAGS) cdhit.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit + + cd-hit-2d: cdhit-common.o cdhit-utility.o cdhit-2d.o +- $(CC) $(CCFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d ++ $(CXX) $(CCFLAGS) cdhit-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-2d + + cd-hit-est: cdhit-common.o cdhit-utility.o cdhit-est.o +- $(CC) $(CCFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est ++ $(CXX) $(CCFLAGS) cdhit-est.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est + + cd-hit-est-2d: cdhit-common.o cdhit-utility.o cdhit-est-2d.o +- $(CC) $(CCFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d ++ $(CXX) $(CCFLAGS) cdhit-est-2d.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-est-2d + + cd-hit-div: cdhit-common.o cdhit-utility.o cdhit-div.o +- $(CC) $(CCFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div ++ $(CXX) $(CCFLAGS) cdhit-div.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-div + + cd-hit-454: cdhit-common.o cdhit-utility.o cdhit-454.o +- $(CC) $(CCFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-454 ++ $(CXX) $(CCFLAGS) cdhit-454.o cdhit-common.o cdhit-utility.o $(LDFLAGS) cd-hit-454 + + # objects + cdhit-common.o: cdhit-common.c++ cdhit-common.h +- $(CC) $(CCFLAGS) cdhit-common.c++ -c ++ $(CXX) $(CCFLAGS) cdhit-common.c++ -c + + cdhit-utility.o: cdhit-utility.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit-utility.c++ -c ++ $(CXX) $(CCFLAGS) cdhit-utility.c++ -c + + cdhit.o: cdhit.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit.c++ -c ++ $(CXX) $(CCFLAGS) cdhit.c++ -c + + cdhit-2d.o: cdhit-2d.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit-2d.c++ -c ++ $(CXX) $(CCFLAGS) cdhit-2d.c++ -c + + cdhit-est.o: cdhit-est.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit-est.c++ -c ++ $(CXX) $(CCFLAGS) cdhit-est.c++ -c + + cdhit-est-2d.o: cdhit-est-2d.c++ cdhit-utility.h +- $(CC) $(CCFLAGS) cdhit-est-2d.c++ -c ++ $(CXX) $(CCFLAGS) cdhit-est-2d.c++ -c + + cdhit-div.o: cdhit-div.c++ cdhit-common.h +- $(CC) $(CCFLAGS) cdhit-div.c++ -c ++ $(CXX) $(CCFLAGS) cdhit-div.c++ -c + + cdhit-454.o: cdhit-454.c++ cdhit-common.h +- $(CC) $(CCFLAGS) cdhit-454.c++ -c ++ $(CXX) $(CCFLAGS) cdhit-454.c++ -c + +-PREFIX ?= /usr/local/bin ++PREFIX ?= /usr/local + + install: ++ mkdir -p $(DESTDIR)$(PREFIX)/bin + for prog in $(PROGS); do \ +- install -m 0755 $$prog $(PREFIX); \ ++ install -m 0755 $$prog $(DESTDIR)$(PREFIX)/bin; \ + done +- install -m 0755 *.pl $(PREFIX); ++ install -m 0755 *.pl $(DESTDIR)$(PREFIX)/bin Modified: head/biology/cd-hit/pkg-plist ============================================================================== --- head/biology/cd-hit/pkg-plist Thu Mar 14 23:53:47 2019 (r495745) +++ head/biology/cd-hit/pkg-plist Thu Mar 14 23:59:47 2019 (r495746) @@ -1,7 +1,9 @@ +bin/FET.pl bin/cd-hit bin/cd-hit-2d bin/cd-hit-2d-para.pl bin/cd-hit-454 +bin/cd-hit-clstr_2_blm8.pl bin/cd-hit-div bin/cd-hit-div.pl bin/cd-hit-est @@ -11,6 +13,8 @@ bin/clstr2tree.pl bin/clstr2txt.pl bin/clstr2xml.pl bin/clstr_cut.pl +bin/clstr_list.pl +bin/clstr_list_sort.pl bin/clstr_merge.pl bin/clstr_merge_noorder.pl bin/clstr_quality_eval.pl